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Part 1: Document Description
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Citation |
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Title: |
GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases |
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Identification Number: |
doi:10.18419/darus-817 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2021-05-03 |
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Version: |
1 |
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Bibliographic Citation: |
Buchholz, Patrick C. F., 2021, "GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases", https://doi.org/10.18419/darus-817, DaRUS, V1 |
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Citation |
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Title: |
GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases |
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Identification Number: |
doi:10.18419/darus-817 |
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Authoring Entity: |
Buchholz, Patrick C. F. (Universität Stuttgart) |
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Distributor: |
DaRUS |
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Access Authority: |
Pleiss, Jürgen |
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Depositor: |
Buchholz, Patrick C. F. |
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Date of Deposit: |
2020-07-01 |
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Holdings Information: |
https://doi.org/10.18419/darus-817 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, alignment, network, amino acid sequence, graph, protein sequence |
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Abstract: |
Protein sequence network for homologues of arylsulfatases and phosphonate monoester hydrolases, including reconstructed ancestral sequences from a maximum-likelihood phylogenetic tree. |
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Notes: |
The GraphML attributes for the edges comprise the edge weights (pairwise sequence identity, "weight"). The GraphML attributes for the nodes comprise several annotations, if available: the annotated name ("Annotation"), the source organism ("Organism"), the accessions from the Protein Data Bank ("PDB"), an accession to public sequence databases such as the NCBI GenBank ("Accession"), an annotated name for the sequence ("Name"), and the group it belongs to ("Group"). Reconstructed ancestors are labelled by an integer as "Name" and "reconstructed ancestor" as "Annotation". |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
van Loo B, Schober M, Valkov E, Heberlein M, Bornberg-Bauer E, Faber K, et al. Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. J Mol Biol. 2018;430: 1004-1023. <a href="https://doi.org/10.1016/j.jmb.2018.02.010">doi:10.1016/j.jmb.2018.02.010</a> |
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van Loo B, Bayer CD, Fischer G, Jonas S, Valkov E, Mohamed MF, et al. Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. J Am Chem Soc. 2019;141: 370-387. <a href="https://doi.org/10.1021/jacs.8b10290">doi:10.1021/jacs.8b10290</a> |
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Data Access |
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Other Study Description Materials |
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Related Studies |
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<a href="https://doi.org/10.18419/darus-1801">https://doi.org/10.18419/darus-1801</a> |
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Related Publications |
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Citation |
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Title: |
Patrick C. F. Buchholz, Bert van Loo, Bernard D. G. Eenink, Erich Bornberg-Bauer, Jürgen Pleiss: "Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation" (submitted) |
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Bibliographic Citation: |
Patrick C. F. Buchholz, Bert van Loo, Bernard D. G. Eenink, Erich Bornberg-Bauer, Jürgen Pleiss: "Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation" (submitted) |
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Label: |
AS_PMH_ancestors.graphml |
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Text: |
GraphML formatted file for an undirected graph (network) containing 238 nodes connected by 28,203 edges. |
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Notes: |
text/xml-graphml |